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The structure of the omega aminotransferase from Pseudomonas aeruginosa
Analyse The structure of the omega aminotransferase from Pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B9B
- Type
- protein
- Length
- 3,486 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.64
- Source
- PSEUDOMONAS AERUGINOSA
- Molecule
- Beta-alanine-pyruvate transaminase
- EC
- 2.6.1.18
- UniProt
- A3LGU8
- Ligands
- PLP, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.64 · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, H | Beta-alanine-pyruvate transaminase (EC 2.6.1.18) | protein | 436 | 40% helix, 18% strand | A3LGU8 |
| B, E | Beta-alanine-pyruvate transaminase (EC 2.6.1.18) | protein | 435 | 40% helix, 18% strand | A3LGU8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 4 copies · chains C, E, D, F, A, G, B, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 10 copies · chains A, G, B, H, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.85 | 0.96 | 58 | empty |
| 2 | 324 | 0.85 | 0.96 | 61 | empty |
| 3 | 319 | 0.85 | 0.96 | 56 | empty |
| 4 | 300 | 0.85 | 0.96 | 55 | empty |
| 5 | 681 | 0.78 | 0.82 | 71 | CL, PLP |
Interfaces
14 interfaces between chains.
- G–H · 6142 Ų buried · 90 hydrogen bonds · protein-protein
- C–D · 6121 Ų buried · 95 hydrogen bonds · protein-protein
- E–F · 6121 Ų buried · 96 hydrogen bonds · protein-protein
- A–B · 6044 Ų buried · 90 hydrogen bonds · protein-protein
- B–H · 903 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4B9B · The structure of the omega aminotransferase from pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A3LGU8
- Elsewhere: RCSB PDB 4B9B · PDBe 4B9B · UniProt A3LGU8
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